Modeling ?-lactam interactions in aqueous solution through combined quantum mechanics-molecular mechanics methods

Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations

Special care is needed in carrying out combined quantum mechanical and molecular mechanical (QM/MM) calculations if the QM/MM boundary passes through a covalent bond. The present paper discusses the importance of correctly handling the MM partial point charges at the QM/MM boundary, and in particular, it contributes in two aspects: (1) Two schemes, namely, the redistributed charge (RC) scheme and the redistributed charge and dipole (RCD) scheme, are introduced to handle link atoms in QM/MM calculations. In both schemes, the point charge at the MM boundary atom that is replaced by the link atom is redistributed to the midpoint of the bonds that connect the MM boundary atom and its neighboring MM atoms. These redistributed charges serve as classical mimics for the auxiliary orbitals associated with the MM host atom in the generalized hybrid orbital (GHO) method. In the RCD scheme, the dipoles of these bonds are preserved by further adjustment of the values of the redistributed charges. The treatments are justified as classical analogues of the QM description given by the GHO method. (2) The new methods are compared quantitatively to similar methods that were suggested by previous work, namely, a shifted-charge scheme and three eliminated-charge schemes. The comparisons were carried out for a series of molecules in terms of proton affinities and geometries. Point charges derived from various charge models were tested. The results demonstrate that it is critical to preserve charge and bond dipole and that it is important to use accurate MM point charges in QM/MM boundary treatments. The RCD scheme was further applied to study the H atom transfer reaction CH3 + CH3CH2CH2OH --> CH4 + CH2CH2CH2OH. Various QM levels of theory were tested to demonstrate the generality of the methodology. It is encouraging to find that the QM/MM calculations obtained a reaction energy, barrier height, saddle-point geometry, and imaginary frequency at the saddle point in quite good agreement with full QM calculations at the same level. Furthermore, analysis based on energy decomposition revealed the quantitatively similar interaction energies between the QM and the MM subsystems for the reactant, for the saddle point, and for the product. These interaction energies almost cancel each other energetically, resulting in negligibly small net effects on the reaction energy and barrier height. However, the charge distribution of the QM atoms is greatly affected by the polarization effect of the MM point charges. The QM/MM charge distribution agrees much better with full QM results than does the unpolarized charge distribution of the capped primary subsystem.

Quantum mechanical methods for enzyme kinetics

This review discusses methods for the incorporation of quantum mechanical effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model. We emphasize three aspects: (a) use of quantum mechanical electronic structure methods such as molecular orbital theory and density functional theory, usually in conjunction with molecular mechanics; (b) treating vibrational motions quantum mechanically, either in an instantaneous harmonic approximation, or by path integrals, or by a three-dimensional wave function coupled to classical nuclear motion; (c) incorporation of multidimensional tunneling approximations into reaction rate calculations.

Water-assisted alkaline hydrolysis of monobactams: a theoretical study

A theoretical study of the water-assisted alkaline hydrolysis of 2-azetidinone, 3-formylamino-2-azetidinone and 3-formylamino-2-azetidine-1-sulfonate ion is carried out at the B3LYP/6-31+G* level. The effect of bulk solvent is taken into account using the PCM solvation model while specific solvent effects are represented by the inclusion of an ancillary water molecule along the reaction profile. The calculated free energy barriers in solution are in reasonable agreement with experimental values. The observed substituent effects due to the presence of the 3-formylamino and the SO(3) groups attached to the beta-lactam ring are crucial factors determining the hydrolysis of monobactam antibiotics.